Merge pull request #1082 from sys-bio/develop

Release 2.3.2
sys-bio · Feb 22, 2023 · a2b213d · a2b213d
2 parents 8fa22f4 + 09031bd
commit a2b213d
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -9,7 +9,7 @@ cmake_minimum_required(VERSION 3.16)
 
 set(ROADRUNNER_VERSION_MAJOR 2)
 set(ROADRUNNER_VERSION_MINOR 3)
-set(ROADRUNNER_VERSION_PATCH 1)
+set(ROADRUNNER_VERSION_PATCH 2)
 
 set(ROADRUNNER_VERSION "${ROADRUNNER_VERSION_MAJOR}.${ROADRUNNER_VERSION_MINOR}.${ROADRUNNER_VERSION_PATCH}")
 

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -973,7 +973,7 @@ stages:
               PythonName: py311
         pool:
           vmImage: 'ubuntu-20.04'
-        container: sysbiouw/roadrunner-manylinux2014-base:latest
+        container: sysbiouw/roadrunner-manylinux2014:latest
         variables:
           CCACHE_DIR: '$(Pipeline.Workspace)/ccache'
           BUILD_DIRECTORY: '$(System.DefaultWorkingDirectory)/build'
@@ -1068,8 +1068,8 @@ stages:
               $(PipExecutable) install -r $(SOURCE_DIR)/requirements.txt
               $(PipExecutable) install -r $(SOURCE_DIR)/test-requirements.txt
 
-              echo "cmake command: cmake -DLLVM_INSTALL_PREFIX=/install-llvm-13.x -DRR_DEPENDENCIES_INSTALL_PREFIX=/libroadrunner-deps/install-libroadrunner-deps -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIRECTORY) -DBUILD_PYTHON=ON -DBUILD_RR_PLUGINS=ON -DBUILD_TESTS=ON -DPython_ROOT_DIR=$(PythonRoot) -DSWIG_EXECUTABLE=$(SwigExecutable) -DCMAKE_BUILD_TYPE=Release .."
-              cmake -DLLVM_INSTALL_PREFIX=/install-llvm-13.x -DRR_DEPENDENCIES_INSTALL_PREFIX=/libroadrunner-deps/install-libroadrunner-deps -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIRECTORY) -DBUILD_PYTHON=ON -DBUILD_RR_PLUGINS=ON -DBUILD_TESTS=ON -DPython_ROOT_DIR=$(PythonRoot) -DSWIG_EXECUTABLE=$(SwigExecutable) -DCMAKE_BUILD_TYPE=Release ..
+              echo "cmake command: cmake -DLLVM_INSTALL_PREFIX=/install-llvm-13.x -DRR_DEPENDENCIES_INSTALL_PREFIX=/install-libroadrunner-deps -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIRECTORY) -DBUILD_PYTHON=ON -DBUILD_RR_PLUGINS=ON -DBUILD_TESTS=ON -DPython_ROOT_DIR=$(PythonRoot) -DSWIG_EXECUTABLE=$(SwigExecutable) -DCMAKE_BUILD_TYPE=Release .."
+              cmake -DLLVM_INSTALL_PREFIX=/install-llvm-13.x -DRR_DEPENDENCIES_INSTALL_PREFIX=/install-libroadrunner-deps -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIRECTORY) -DBUILD_PYTHON=ON -DBUILD_RR_PLUGINS=ON -DBUILD_TESTS=ON -DPython_ROOT_DIR=$(PythonRoot) -DSWIG_EXECUTABLE=$(SwigExecutable) -DCMAKE_BUILD_TYPE=Release ..
               cmake --build . --target install --config Release -j 12
 
             displayName: Build With Python

diff --git a/docker/roadrunner-manylinux2014-add-deps/Dockerfile b/docker/roadrunner-manylinux2014-add-deps/Dockerfile
@@ -0,0 +1,35 @@
+# This dockerfile contains commands for a base environment suitable for
+# building manylinux pip wheels.
+# The default gcc/g++ is 9.3
+# Conda is used to manage Python versions.
+#
+# This dockerfile installs roadrunner dependencies and llvm package
+# But does not build roadrunner, which is the subject of another dockerfile
+
+FROM sysbiouw/roadrunner-manylinux2014-base
+
+#RUN git clone https://github.com/sys-bio/llvm-13.x.git \
+#    && cd llvm-13.x
+#RUN cd /llvm-13.x/llvm && mkdir build && cd build \
+#    && cmake -DCMAKE_INSTALL_PREFIX=/install-llvm-13.x -DCMAKE_BUILD_TYPE=Release ..
+#RUN cd /llvm-13.x/llvm/build \
+#    && cmake --build . --target install --config Release -j 12
+#RUN rm -rf /llvm-13.x
+#
+#RUN git clone https://github.com/sys-bio/libroadrunner-deps.git --recurse-submodules
+#RUN cd libroadrunner-deps && mkdir build && cd build \
+#    && cmake -DCMAKE_INSTALL_PREFIX=../install-libroadrunner-deps -DCMAKE_BUILD_TYPE=Release .. \
+#    && cmake --build . --target install --config Release -j 12
+
+#Run above to re-create build; for now, just use pre-built:
+
+RUN wget https://github.com/sys-bio/llvm-13.x/releases/download/llvmorg-13.0.0/llvm-13.x-manylinux2014.tgz \
+    && tar -xvf llvm-13.x-manylinux2014.tgz \
+    && rm llvm-13.x-manylinux2014.tgz
+
+RUN wget https://github.com/sys-bio/libroadrunner-deps/releases/download/v2.1/libroadrunner-deps-manylinux2014-Release.zip \
+    && unzip libroadrunner-deps-manylinux2014-Release.zip \
+    && rm libroadrunner-deps-manylinux2014-Release.zip \
+    && mv libroadrunner-deps-manylinux2014-Release/install-azure/Release install-libroadrunner-deps
+
+
diff --git a/docker/roadrunner-manylinux2014-base/Dockerfile b/docker/roadrunner-manylinux2014-base/Dockerfile
@@ -21,23 +21,6 @@ RUN cd .. && rm -rf gcc-11.1.0
 
 RUN yum install -y nano
 
-RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
-RUN bash Miniconda3-latest-Linux-x86_64.sh -b -p /Miniconda3
-
-RUN /Miniconda3/bin/conda create -y --name py37 python=3.7 pytest
-RUN /Miniconda3/bin/conda create -y --name py38 python=3.8 pytest
-RUN /Miniconda3/bin/conda create -y --name py39 python=3.9 pytest
-
-RUN /Miniconda3/bin/conda init && bash ~/.bashrc && . ~/.bashrc
-
-RUN git clone https://github.com/sys-bio/llvm-13.x.git \
-    && cd llvm-13.x
-RUN cd /llvm-13.x/llvm && mkdir build && cd build \
-    && cmake -DCMAKE_INSTALL_PREFIX=/install-llvm-13.x -DCMAKE_BUILD_TYPE=Release ..
-RUN cd /llvm-13.x/llvm/build \
-    && cmake --build . --target install --config Release -j 12
-RUN rm -rf /llvm-13.x
-
 RUN yum install -y pcre-devel.x86_64
 
 ENV swig_source_dir /swig-4.0.2
@@ -73,31 +56,4 @@ RUN useradd -m user \
   && yes password | passwd user
 RUN yum install -y initscripts
 
-RUN git clone https://github.com/sys-bio/libroadrunner-deps.git --recurse-submodules
-RUN cd libroadrunner-deps && mkdir build && cd build \
-    && cmake -DCMAKE_INSTALL_PREFIX=../install-libroadrunner-deps -DCMAKE_BUILD_TYPE=Release .. \
-    && cmake --build . --target install --config Release -j 12
-
-
-RUN printf "#!bin/bash \n\
-/Miniconda3/envs/py39/bin/pip install numpy\n\
-if [ ! -d /roadrunner ]; then\n\
-	git clone https://github.com/sys-bio/roadrunner.git\n\
-fi\n\
-cd /roadrunner\n\
-mkdir build\n\
-cd build\n\
-cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_RR_PLUGINS=ON -DCMAKE_INSTALL_PREFIX=../../Roadrunner-release -DRR_DEPENDENCIES_INSTALL_PREFIX=/libroadrunner-deps/install-libroadrunner-deps -DLLVM_INSTALL_PREFIX=/install-llvm-13.x -DBUILD_TESTS=ON -DBUILD_PYTHON=ON -DSWIG_EXECUTABLE=/swig-4.0.2/swig -DPython_ROOT_DIR=/Miniconda3/envs/py39 ..\n\
-cmake --build . --target install --config Release -j 16\n" > /build-roadrunner.sh
-
-# install valgrind
-RUN wget https://sourceware.org/pub/valgrind/valgrind-3.18.1.tar.bz2 --no-check-certificate \
-    && tar -xvf valgrind-3.18.1.tar.bz2\
-    && cd valgrind-3.18.1/\
-    && mkdir build\
-    && cd build\
-    && ../configure                                                \
-    && make -j 12\
-    && make install
-
 RUN yum install -y qt5-qtbase-devel check
diff --git a/docker/roadrunner-manylinux2014-build/Dockerfile b/docker/roadrunner-manylinux2014-build/Dockerfile
diff --git a/docker/roadrunner-manylinux2014/Dockerfile b/docker/roadrunner-manylinux2014/Dockerfile
@@ -0,0 +1,19 @@
+# This dockerfile contains commands for a base environment suitable for
+# building manylinux pip wheels.
+# The default gcc/g++ is 9.3
+# Conda is used to manage Python versions.
+#
+# This dockerfile installs roadrunner dependencies and llvm package
+# But does not build roadrunner, which is the subject of another dockerfile
+
+FROM sysbiouw/roadrunner-manylinux2014-add-deps
+
+RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+RUN bash Miniconda3-latest-Linux-x86_64.sh -b -p /Miniconda3
+
+RUN /Miniconda3/bin/conda create -y --name py38 python=3.8 pytest
+RUN /Miniconda3/bin/conda create -y --name py39 python=3.9 pytest
+RUN /Miniconda3/bin/conda create -y --name py310 python=3.10 pytest
+RUN /Miniconda3/bin/conda create -y --name py311 python=3.11 pytest -c conda-forge
+
+RUN /Miniconda3/bin/conda init && bash ~/.bashrc && . ~/.bashrc
diff --git a/docs/docs-build/C++APIReference/CVODEIntegrator.html b/docs/docs-build/C++APIReference/CVODEIntegrator.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" >
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>CVODEIntegrator &mdash; libRoadRunner 1.1.16 documentation</title>
@@ -30,11 +30,15 @@
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
         <div class="wy-side-nav-search" >
-            <a href="../index.html" class="icon icon-home"> libRoadRunner
+
+
+
+          <a href="../index.html" class="icon icon-home">
+            libRoadRunner
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" />
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
     <input type="hidden" name="check_keywords" value="yes" />
     <input type="hidden" name="area" value="default" />
   </form>
@@ -120,7 +124,7 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="../index.html" class="icon icon-home"></a></li>
+      <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
           <li class="breadcrumb-item"><a href="index.html">The LibRoadRunner C++ Library</a></li>
       <li class="breadcrumb-item active">CVODEIntegrator</li>
       <li class="wy-breadcrumbs-aside">

diff --git a/docs/docs-build/C++APIReference/Dictionary.html b/docs/docs-build/C++APIReference/Dictionary.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" >
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Dictionary &mdash; libRoadRunner 1.1.16 documentation</title>
@@ -30,11 +30,15 @@
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
         <div class="wy-side-nav-search" >
-            <a href="../index.html" class="icon icon-home"> libRoadRunner
+
+
+
+          <a href="../index.html" class="icon icon-home">
+            libRoadRunner
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" />
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
     <input type="hidden" name="check_keywords" value="yes" />
     <input type="hidden" name="area" value="default" />
   </form>
@@ -120,7 +124,7 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="../index.html" class="icon icon-home"></a></li>
+      <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
           <li class="breadcrumb-item"><a href="index.html">The LibRoadRunner C++ Library</a></li>
       <li class="breadcrumb-item active">Dictionary</li>
       <li class="wy-breadcrumbs-aside">